Merge pull request #751 from naik-aakash/fix_phonon_flow

[WIP] Fix phonon + Lobster flow

docs/user/codes/vasp.md

@@ -232,6 +232,12 @@ converted into a dynamical matrix. To correct for polarization effects, a correc
 dynamical matrix based on BORN charges can be performed. Finally, phonon densities of states,
 phonon band structures and thermodynamic properties are computed.
 
+```{warning}
+The current implementation of the workflow does not consider the initial magnetic moments
+for the determination of the symmetry of the structure; therefore, they are removed from the structure.
+```
+
+
 ```{note}
 It is heavily recommended to symmetrize the structure before passing it to
 this flow. Otherwise, a different space group might be detected and too

pyproject.toml

@@ -78,17 +78,17 @@ strict = [
     "emmet-core==0.78.0rc4",
     "ijson==3.2.3",
     "jobflow==0.1.17",
-    "lobsterpy==0.3.6",
+    "lobsterpy==0.3.8",
     "mace-torch>=0.3.3",
     "matgl==1.0.0",
     "monty==2024.2.2",
-    "mp-api==0.40.1",
+    "mp-api==0.40.2",
     "numpy",
     "phonopy==2.21.2",
     "pydantic-settings==2.2.1",
     "pydantic==2.6.2",
     "pymatgen-analysis-defects==2024.2.24",
-    "pymatgen==2023.12.18",
+    "pymatgen==2024.2.23",
     "quippy-ase==0.9.14",
     "seekpath==2.1.0",
     "typing-extensions==4.10.0",

src/atomate2/common/jobs/phonons.py

@@ -4,6 +4,7 @@
 
 import contextlib
 import logging
+import warnings
 from dataclasses import dataclass, field
 from typing import TYPE_CHECKING
 
@@ -150,7 +151,16 @@ def generate_phonon_displacements(
     code:
         code to perform the computations
     """
-    cell = get_phonopy_structure(structure)
+    warnings.warn(
+        "Initial magnetic moments will not be considered for the determination "
+        "of the symmetry of the structure and thus will be removed now.",
+        stacklevel=1,
+    )
+    cell = get_phonopy_structure(
+        structure.remove_site_property(property_name="magmom")
+        if "magmom" in structure.site_properties
+        else structure
+    )
     if code == "vasp":
         factor = VaspToTHz
     # a bit of code repetition here as I currently
@@ -226,7 +236,9 @@ def generate_frequencies_eigenvectors(
         Additional parameters that are passed to PhononBSDOSDoc.from_forces_born
     """
     return PhononBSDOSDoc.from_forces_born(
-        structure=structure,
+        structure=structure.remove_site_property(property_name="magmom")
+        if "magmom" in structure.site_properties
+        else structure,
         supercell_matrix=supercell_matrix,
         displacement=displacement,
         sym_reduce=sym_reduce,